Well, when you consider that snakes are shipped in cardboard boxes with no holes and tight styrofoam padding, and deli containers don't have very big holes or very many, and snakes being sold spend several days in them sometimes, I'd guess that your holes don't need to be all that large, but placement is probably more important - you do want good cross-ventiliation. You also don't want holes so big that your snake can push his way out. My snake lives in tank with a mesh top, but his travel bin has three small (about 1/4") holes on each side. Never had issues with it.
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